Sequence
atgc intronic sequence ATGC exonic sequence...ctgggattgagaacgctttgaatgttggtgattcccattttgctaaaaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07340.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G386614_T01 (Zea mays), 3'ss of exon 2
-----ctgggattgagaacgctt-tgaatgttggtgattcccattttgc---taaaaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
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gttagctgtgactttcactccctattttttttggacaaaaactttcagcccctaaaaaacttcttgtgaaacatttttg---------aacttatagtcgatttgacagGACAAGTCTTCTACCTCCAACCTGAAGATTGAAGCACTTGTATTAACAAGGCTTGTTATGGCTTCACATTCGCCATCTGTGTTTCATCCATACAT-CAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G168629_T04 (Zea mays), 3'ss of exon 13
-----ctgggattgagaacgctttgaatgttggtgattcccattttgctaa-aaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
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gttagctgtgactttcactccctatttttttggacaaaaactttcagcccttaaaaaacttcttgtgaaaccatt-----tttttaacttagt--cgatttgacagGACAAGTCTTCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTAACAAGGCTTGTTATGGCTTCACATTCACCATCTGTGTTTCATCCATACATCAAG
upper sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G053644_T02 (Zea mays), 3'ss of exon 11
-----ctgggattgagaacgctttgaat--gttggtgattcccattttgctaaaaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
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gttagctgtgactttcactccctttttttggacaaaaactttcagccc-ctaaaaaacttcttgtgaaacatttttg---------aacttatagtcgatttgacagGACAAGTCTTCTACCTCCAACCTGAAGATTGAAGCACTTGTATTAACAAGGCTTGTTATGGCTTCACATTCGCCATCTGTGTTTCATCCATACATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
tgctaac putative branch site (score: 1)
cttgttttctttttca CT-rich tract
ttttctttttcata TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgggattgagaacgctttgaatgttggtgattcccattttgctaaaaaagattatgtgcaggacttctacttgttgctaacttgttttctttttcatagGATAAGTCATCTACCTCCAACCTGAAGATTGAAGCCCTTGTATTTACAAGACTTGTTATGGCTTCACATTCCCCAGCTGTGTTTCATCCATACATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - -gttggtg
- - - - - - - - - - - - - - - - - - attttgc
- - - - - - - - - - - - - - - - - - - -ttgctaa
- - - - - - - - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcagg